PDB-4bht: Structural Determinants of Cofactor Specificity and Domain Flexib...

ID or keywords:

Entry

Database: PDB / ID: 4bht

Title

Structural Determinants of Cofactor Specificity and Domain Flexibility in Bacterial Glutamate Dehydrogenases

Components

NADP-SPECIFIC GLUTAMATE DEHYDROGENASE

Keywords

OXIDOREDUCTASE

Function / homology

Function and homology information

glutamate dehydrogenase complex / glutamate dehydrogenase (NADP+) / glutamate metabolic process / glutamate biosynthetic process / glutamate dehydrogenase (NADP+) activity / guanosine tetraphosphate binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function

Biological species

ESCHERICHIA COLI (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

Oliveira, T. / Sharkey, M. / Engel, P. / Khan, A.

Citation

Journal: FEBS J. / Year: 2013
Title: Structure of Nadp(+) -Dependent Glutamate Dehydrogenase from Escherichia Coli: Reflections on the Basis of Coenzyme Specificity in the Family of Glutamate Dehydrogenases.
Authors: Sharkey, M.A. / Oliveira, T.F. / Engel, P.C. / Khan, A.R.

History

Deposition	Apr 6, 2013	Deposition site: PDBE / Processing site: PDBE
Supersession	Jun 19, 2013	ID: 2YFG
Revision 1.0	Jun 19, 2013	Provider: repository / Type: Initial release
Revision 1.1	Jul 3, 2013	Group: Atomic model / Other
Revision 1.2	Jul 24, 2013	Group: Atomic model
Revision 1.3	Aug 7, 2013	Group: Database references
Revision 1.4	Sep 11, 2013	Group: Database references
Revision 1.5	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4bht.cif.gz	1.4 MB	Display	PDBx/mmCIF format
PDB format	pdb4bht.ent.gz	1.2 MB	Display	PDB format
PDBx/mmJSON format	4bht.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4bht_validation.pdf.gz	511.9 KB	Display	wwPDB validaton report
Full document	4bht_full_validation.pdf.gz	551 KB	Display
Data in XML	4bht_validation.xml.gz	100.9 KB	Display
Data in CIF	4bht_validation.cif.gz	140.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bh/4bht ftp://data.pdbj.org/pub/pdb/validation_reports/bh/4bht	HTTPS FTP

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Related structure data

Related structure data	1bvgS S: Starting model for refinement
Similar structure data	4fcc-2 3sbo-d 2tmg-d 4fcc-1 1euz-d 6yei-d 4fhn-3 6yeh-d 5xvi-d 1gtm-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: NADP-SPECIFIC GLUTAMATE DEHYDROGENASE

B: NADP-SPECIFIC GLUTAMATE DEHYDROGENASE

C: NADP-SPECIFIC GLUTAMATE DEHYDROGENASE

D: NADP-SPECIFIC GLUTAMATE DEHYDROGENASE

E: NADP-SPECIFIC GLUTAMATE DEHYDROGENASE

F: NADP-SPECIFIC GLUTAMATE DEHYDROGENASE

hetero molecules

294 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	100.975, 152.861, 169.366
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	NADP-SPECIFIC GLUTAMATE DEHYDROGENASE Mass: 48635.215 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PTAC-85 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TG1 References: UniProt: P00370, glutamate dehydrogenase (NADP+)
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₈N₂O₄S / Comment: pH buffer*YM
#4: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 773 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.2 Å³/Da / Density % sol: 45.2 % / Description: NONE
Crystal grow	Details: 15-25% PEG 3350, 0.1M HEPES/TRIS PH 7-8, 0.2M NACL

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Details: MIRRORS
Radiation	Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9792 Å / Relative weight: 1
Reflection	Resolution: 2.5→46.9 Å / Num. obs: 91251 / % possible obs: 99.8 % / Redundancy: 5.9 % / R_merge(I) obs: 0.01 / Net I/σ(I): 18.1
Reflection shell	Resolution: 2.5→2.59 Å / Redundancy: 4.3 % / R_merge(I) obs: 0.5 / Mean I/σ(I) obs: 3 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE: 1.8.2_1309)	refinement
DENZO		data reduction
SCALEPACK		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BVG

1bvg

Resolution: 2.5→46.9 Å / SU ML: 0.29 / σ(F): 0.08 / Phase error: 24.13 / Stereochemistry target values: MLHL

	R_factor	Num. reflection	% reflection
R_free	0.2268	4556	5 %
R_work	0.1592	-	-
obs	0.1626	91068	99.84 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.5→46.9 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	20181	0	136	773	21090

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.015	20752
X-RAY DIFFRACTION	f_angle_d	1.592	27978
X-RAY DIFFRACTION	f_dihedral_angle_d	14.745	7608
X-RAY DIFFRACTION	f_chiral_restr	0.077	3023
X-RAY DIFFRACTION	f_plane_restr	0.01	3685

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.5-2.5284	0.3185	158	0.2062	2856	X-RAY DIFFRACTION	100
2.5284-2.5582	0.3145	145	0.2037	2840	X-RAY DIFFRACTION	100
2.5582-2.5894	0.2867	140	0.1986	2887	X-RAY DIFFRACTION	100
2.5894-2.6221	0.2747	161	0.1915	2814	X-RAY DIFFRACTION	100
2.6221-2.6566	0.3075	164	0.1987	2874	X-RAY DIFFRACTION	100
2.6566-2.693	0.2776	157	0.1879	2838	X-RAY DIFFRACTION	100
2.693-2.7315	0.2662	151	0.1806	2878	X-RAY DIFFRACTION	100
2.7315-2.7723	0.2729	167	0.1771	2817	X-RAY DIFFRACTION	100
2.7723-2.8156	0.2663	146	0.1787	2861	X-RAY DIFFRACTION	100
2.8156-2.8617	0.2797	149	0.1768	2845	X-RAY DIFFRACTION	100
2.8617-2.9111	0.2352	160	0.1694	2840	X-RAY DIFFRACTION	100
2.9111-2.964	0.2526	183	0.1711	2876	X-RAY DIFFRACTION	100
2.964-3.021	0.3098	144	0.175	2835	X-RAY DIFFRACTION	100
3.021-3.0826	0.2748	130	0.181	2933	X-RAY DIFFRACTION	100
3.0826-3.1497	0.2517	164	0.1798	2827	X-RAY DIFFRACTION	100
3.1497-3.2229	0.2379	135	0.1704	2873	X-RAY DIFFRACTION	100
3.2229-3.3035	0.2729	161	0.1632	2874	X-RAY DIFFRACTION	100
3.3035-3.3928	0.2524	140	0.1653	2907	X-RAY DIFFRACTION	100
3.3928-3.4926	0.2643	157	0.167	2847	X-RAY DIFFRACTION	100
3.4926-3.6053	0.2123	147	0.1597	2905	X-RAY DIFFRACTION	100
3.6053-3.7341	0.194	136	0.1499	2902	X-RAY DIFFRACTION	100
3.7341-3.8835	0.1896	154	0.1393	2891	X-RAY DIFFRACTION	100
3.8835-4.0602	0.1799	169	0.1281	2877	X-RAY DIFFRACTION	100
4.0602-4.2741	0.1795	158	0.1232	2874	X-RAY DIFFRACTION	100
4.2741-4.5417	0.1691	133	0.1258	2928	X-RAY DIFFRACTION	100
4.5417-4.892	0.1757	143	0.1235	2923	X-RAY DIFFRACTION	100
4.892-5.3837	0.1887	154	0.1434	2927	X-RAY DIFFRACTION	100
5.3837-6.1612	0.2098	145	0.1603	2956	X-RAY DIFFRACTION	100
6.1612-7.7568	0.2193	151	0.1741	2985	X-RAY DIFFRACTION	100
7.7568-46.9081	0.2105	154	0.1723	3022	X-RAY DIFFRACTION	97

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	0.6696	0.2518	-0.0388	0.2381	0.0225	0.3664	0.012	-0.0526	-0.114	0.047	0.0221	0.0455	0.1305	-0.0923	-0.0369	0.3621	-0.0034	0.013	0.294	0.0416	0.2756	-51.0049	-21.5784	26.5466
2	8.7502	0.6049	0.2779	5.685	-3.5808	8.3915	0.1353	-0.604	0.0197	0.6731	0.0635	0.0044	-0.6014	0.2114	-0.0999	0.4813	-0.0395	0.0492	0.3805	-0.0206	0.3539	-70.4988	-19.5458	46.9336
3	1.6573	0.7339	-1.3616	1.5409	-1.0193	2.4105	-0.0745	-0.1582	-0.2755	0.0684	0.0172	-0.1448	0.3765	-0.0254	0.0849	0.2714	-0.0458	-0.0611	0.293	0.0225	0.3129	-62.6348	-30.2678	25.4036
4	0.4051	0.403	0.0524	1.0005	0.1027	0.3431	0.0339	-0.0523	0.0852	0.1151	0.0263	-0.0424	-0.1354	0.0424	-0.0589	0.3481	0.018	0.0081	0.2553	-0.0213	0.2499	-23.9877	21.0205	27.4375
5	6.3724	-1.396	0.9327	4.9734	0.1859	5.4651	0.5681	-0.5318	-1.0088	1.4951	-0.2166	-0.0031	0.7824	-0.2619	-0.2478	0.9254	-0.1443	-0.1303	0.3141	0.0568	0.501	-5.3588	20.105	49.5491
6	0.6992	1.3994	1.4201	2.0106	1.5129	2.3091	-0.1097	-0.0462	0.1004	0.0163	-0.0686	-0.0711	-0.2679	-0.0582	0.2059	0.2844	-0.0245	0.051	0.2875	-0.0307	0.2731	-11.8294	29.7791	26.4451
7	0.7553	-0.1603	0.1777	0.1904	-0.1191	0.1722	-0	-0.0507	-0.1021	0.0875	0.0399	-0.063	0.1217	0.0172	-0.043	0.3634	0.0211	-0.0023	0.2393	-0.0148	0.2896	-15.9828	-19.5137	19.7353
8	4.4944	0.2704	4.1117	1.7644	0.1775	3.8689	0.1823	0.6111	-0.3622	-0.5131	-0.1093	0.0201	-0.1116	0.026	-0.0922	0.3359	0.0344	0.0159	0.3755	-0.0341	0.3548	5.0815	-29.5278	5.3841
9	1.4268	-1.5211	0.0109	2.6258	0.1412	0.4451	-0.1265	-0.1493	-0.0759	0.2677	0.119	0.0092	0.2192	0.1024	0.0203	0.2852	0.0071	-0.0237	0.2456	-0.0076	0.216	-2.437	-20.2086	24.687
10	0.7811	0.407	0.1176	0.7682	-0.5338	1.5221	0.0188	-0.0895	0.1813	0.1537	0.0885	0.2895	-0.2565	-0.2448	-0.1062	0.2763	0.0775	0.0408	0.2512	0.0358	0.3216	-54.8035	17.7751	19.5589
11	0.8161	-0.7671	0.8208	1.393	-0.5381	1.5176	0.0382	0.0268	0.3489	0.2211	0.2871	0.0175	-1.5314	-0.7907	0.0331	1.4421	0.6213	0.1968	0.7232	0.3872	0.4645	-79.4726	30.2794	11.91
12	1.7883	-0.9211	0.6136	1.5855	-0.5136	1.4353	-0.1059	-0.316	0.0217	0.4646	0.5598	0.6284	-1.0428	-0.769	-0.2781	0.6772	0.2324	0.2394	0.5591	0.2784	0.5911	-71.4379	13.2686	25.0671
13	1.0624	-0.2891	-0.147	1.4637	0.1491	0.6289	-0.0213	0.1962	-0.018	-0.3513	0.0081	0.1798	-0.0151	-0.1128	0.0108	0.3227	-0.0516	-0.0446	0.2931	0.0075	0.2101	-47.0945	-5.3868	-11.5528
14	2.8312	-0.0364	0.0265	5.7532	0.0979	4.8932	0.119	0.2802	-0.384	-0.571	-0.1315	0.0212	0.8782	-0.1317	-0.0025	0.4997	-0.0585	-0.1278	0.5155	-0.0152	0.367	-70.6644	-17.1161	-24.2077
15	0.9748	0.4077	0.5582	3.1993	-1.1508	2.9765	0.0379	0.0263	-0.0245	-0.0655	0.0866	0.3858	-0.0574	-0.5487	-0.1179	0.1711	0.0255	0.0204	0.3748	0.0301	0.3026	-65.7882	-0.9741	-7.9547
16	0.8724	-0.1566	-0.0505	1.3073	0.3233	0.5583	-0.0324	0.1965	0.0102	-0.332	0.0634	-0.0873	-0.043	0.0751	-0.0404	0.3359	-0.0641	0.0258	0.2569	0.0018	0.2092	-26.104	4.7416	-11.001
17	3.0869	-0.2673	-1.6022	4.7228	-0.6269	4.2563	0.2851	0.2917	0.3086	-0.7042	0.0392	-0.2084	-0.4745	-0.1205	-0.28	0.4405	-0.0674	0.0748	0.3825	-0.0072	0.3357	1.8819	17.7205	-18.1351
18	2.2905	1.4879	-1.5691	2.0477	-0.6424	2.7875	-0.1652	0.1624	-0.1874	-0.3666	0.1602	-0.2711	-0.0337	0.1143	-0.0046	0.242	-0.0001	-0.0286	0.2489	-0.0051	0.2397	-5.2624	0.6701	-7.5656

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(CHAIN A AND RESID 6:269)
2	X-RAY DIFFRACTION	2	(CHAIN A AND RESID 270:302)
3	X-RAY DIFFRACTION	3	(CHAIN A AND RESID 303:447)
4	X-RAY DIFFRACTION	4	(CHAIN B AND RESID 6:269)
5	X-RAY DIFFRACTION	5	(CHAIN B AND RESID 270:302)
6	X-RAY DIFFRACTION	6	(CHAIN B AND RESID 303:447)
7	X-RAY DIFFRACTION	7	(CHAIN C AND RESID 6:269)
8	X-RAY DIFFRACTION	8	(CHAIN C AND RESID 270:293)
9	X-RAY DIFFRACTION	9	(CHAIN C AND RESID 294:447)
10	X-RAY DIFFRACTION	10	(CHAIN D AND RESID 6:226)
11	X-RAY DIFFRACTION	11	(CHAIN D AND RESID 234:333)
12	X-RAY DIFFRACTION	12	(CHAIN D AND RESID 334:447)
13	X-RAY DIFFRACTION	13	(CHAIN E AND RESID 6:211)
14	X-RAY DIFFRACTION	14	(CHAIN E AND RESID 212:370)
15	X-RAY DIFFRACTION	15	(CHAIN E AND RESID 371:447)
16	X-RAY DIFFRACTION	16	(CHAIN F AND RESID 6:204)
17	X-RAY DIFFRACTION	17	(CHAIN F AND RESID 205:356)
18	X-RAY DIFFRACTION	18	(CHAIN F AND RESID 357:447)

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